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Open Access Database

DIGAP - a Database of Improved Gene Annotation for Phytopathogens

Na Gao2, Ling-Ling Chen12*, Hong-Fang Ji2, Wei Wang2, Ji-Wei Chang1, Bei Gao23, Lin Zhang2, Shi-Cui Zhang3 and Hong-Yu Zhang12*

Author Affiliations

1 National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China

2 Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China

3 Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China

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BMC Genomics 2010, 11:54  doi:10.1186/1471-2164-11-54

Published: 21 January 2010

Abstract

Background

Bacterial plant pathogens are very harmful to their host plants, which can cause devastating agricultural losses in the world. With the development of microbial genome sequencing, many strains of phytopathogens have been sequenced. However, some misannotations exist in these phytopathogen genomes. Our objective is to improve these annotations and store them in a central database DIGAP.

Description

DIGAP includes the following improved information on phytopathogen genomes. (i) All the 'hypothetical proteins' were checked, and non-coding ORFs recognized by the Z curve method were removed. (ii) The translation initiation sites (TISs) of 20% ~ 25% of all the protein-coding genes have been corrected based on the NCBI RefSeq, ProTISA database and an ab initio program, GS-Finder. (iii) Potential functions of about 10% 'hypothetical proteins' have been predicted using sequence alignment tools. (iv) Two theoretical gene expression indices, the codon adaptation index (CAI) and the E(g) index, were calculated to predict the gene expression levels. (v) Potential agricultural bactericide targets and their homology-modeled 3D structures are provided in the database, which is of significance for agricultural antibiotic discovery.

Conclusion

The results in DIGAP provide useful information for understanding the pathogenetic mechanisms of phytopathogens and for finding agricultural bactericides. DIGAP is freely available at http://ibi.hzau.edu.cn/digap/ webcite.